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Asym./Biol. Unit (Jmol Viewer)

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Title :   THE STRUCTURE OF A PUTATIVE MALATE/LACTATE DEHYDROGENASE FROM E. COLI.

Authors :   M. E. Cuff, T. Skarina, A. Edwards, A. Savchenko, M. Cymborowski, W. Min A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   03 Mar 06 (Deposition) - 25 Apr 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A,B

Keywords :   Malate, Lactate, Dehydrogenase, Nad, E. Coli, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Cuff, T. Skarina, A. Edwards, A. Savchenko, M. Cymborowski, W. Minor, A. Joachimiak
The Structure Of A Putative Malate/Lactate Dehydrogenase From E. Coli.
To Be Published
PubMed: search

Molecule 1 - MALATE/L-LACTATE DEHYDROGENASES
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	P11
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YBIC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 37)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
4	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:48 , THR A:162 , ALA A:187 , PHE A:188 , GLY A:189 , NAD A:1001 , SO4 A:1007 , EDO A:1018 , EDO A:1019	BINDING SITE FOR RESIDUE SO4 A 1003
02	AC2	SOFTWARE	ARG A:6 , ARG A:323 , HOH A:1334	BINDING SITE FOR RESIDUE SO4 A 1004
03	AC3	SOFTWARE	HIS B:45 , ASP B:46 , SER B:47 , HIS B:48 , SO4 B:1008 , HOH B:1041 , HOH B:1119 , HOH B:1127 , HOH B:1444	BINDING SITE FOR RESIDUE SO4 B 1005
04	AC4	SOFTWARE	ARG B:58 , ARG B:192 , ALA B:337 , HOH B:1179 , HOH B:1224 , HOH B:1325	BINDING SITE FOR RESIDUE SO4 B 1006
05	AC5	SOFTWARE	HIS A:45 , ASP A:46 , SER A:47 , HIS A:48 , NAD A:1001 , SO4 A:1003 , HOH A:1295 , HOH A:1451	BINDING SITE FOR RESIDUE SO4 A 1007
06	AC6	SOFTWARE	HIS B:48 , PHE B:188 , GLY B:189 , NAD B:1002 , SO4 B:1005 , EDO B:1013 , HOH B:1378 , HOH B:1380 , HOH B:1422	BINDING SITE FOR RESIDUE SO4 B 1008
07	AC7	SOFTWARE	ARG B:320 , GLN B:324 , HOH B:1301	BINDING SITE FOR RESIDUE SO4 B 1009
08	AC8	SOFTWARE	ARG B:21	BINDING SITE FOR RESIDUE SO4 B 1010
09	AC9	SOFTWARE	HIS A:45 , HIS A:48 , HIS A:120 , GLY A:122 , ARG A:123 , ILE A:124 , VAL A:144 , THR A:162 , PRO A:164 , LEU A:178 , LEU A:179 , ASP A:180 , TYR A:181 , ALA A:182 , ALA A:187 , ASN A:270 , GLY A:313 , GLU A:316 , SO4 A:1003 , SO4 A:1007 , EDO A:1019 , HOH A:1023 , HOH A:1025 , HOH A:1071 , HOH A:1112 , HOH A:1138 , HOH A:1256 , HOH A:1295 , HOH A:1312 , HOH A:1347 , PHE B:153 , HIS B:234 , LYS B:235 , TYR B:237 , HOH B:1135 , HOH B:1243	BINDING SITE FOR RESIDUE NAD A 1001
10	BC1	SOFTWARE	PHE A:153 , HIS A:234 , LYS A:235 , TYR A:237 , HOH A:1130 , HIS B:45 , HIS B:48 , HIS B:120 , GLY B:122 , ARG B:123 , ILE B:124 , VAL B:144 , THR B:162 , PRO B:164 , LEU B:178 , LEU B:179 , ASP B:180 , TYR B:181 , ALA B:182 , ALA B:187 , ASN B:270 , GLY B:313 , GLU B:316 , SO4 B:1008 , EDO B:1013 , HOH B:1127 , HOH B:1134 , HOH B:1201 , HOH B:1241 , HOH B:1262 , HOH B:1306 , HOH B:1378	BINDING SITE FOR RESIDUE NAD B 1002
11	BC2	SOFTWARE	GLN A:221 , GLU A:350	BINDING SITE FOR RESIDUE EDO A 1011
12	BC3	SOFTWARE	HIS B:106 , ALA B:134 , GLY B:135 , ASN B:278 , GLU B:280 , HOH B:1034	BINDING SITE FOR RESIDUE EDO B 1012
13	BC4	SOFTWARE	HIS B:48 , HIS B:120 , MSE B:149 , THR B:162 , NAD B:1002 , SO4 B:1008 , HOH B:1374	BINDING SITE FOR RESIDUE EDO B 1013
14	BC5	SOFTWARE	ARG B:6 , GLU B:322 , ARG B:323 , HOH B:1331 , HOH B:1332 , HOH B:1432	BINDING SITE FOR RESIDUE EDO B 1014
15	BC6	SOFTWARE	GLN A:290 , LYS B:254 , HIS B:257 , GLU B:259 , THR B:260 , HOH B:1443	BINDING SITE FOR RESIDUE EDO B 1015
16	BC7	SOFTWARE	GLN A:10 , HOH A:1305 , HOH A:1396 , HOH A:1397 , HOH A:1400 , HOH A:1433	BINDING SITE FOR RESIDUE EDO A 1016
17	BC8	SOFTWARE	HIS A:154 , HOH A:1370 , HOH A:1449 , LYS B:307	BINDING SITE FOR RESIDUE EDO A 1017
18	BC9	SOFTWARE	ARG A:192 , SO4 A:1003 , HOH A:1257	BINDING SITE FOR RESIDUE EDO A 1018
19	CC1	SOFTWARE	HIS A:48 , HIS A:120 , MSE A:149 , THR A:162 , NAD A:1001 , SO4 A:1003	BINDING SITE FOR RESIDUE EDO A 1019
20	CC2	SOFTWARE	SER B:47 , GLY B:189 , ARG B:192 , HOH B:1320	BINDING SITE FOR RESIDUE EDO B 1020
21	CC3	SOFTWARE	TRP A:60 , SER A:61 , HOH A:1043 , HOH A:1342 , HOH A:1355 , HOH A:1358 , HOH A:1398 , HOH A:1418	BINDING SITE FOR RESIDUE 1PE A 1021

(no "SS Bond" information available for 2G8Y)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:223	-	Pro A:224
2	Ser B:223	-	Pro B:224

(no "SAP(SNP)/Variant" information available for 2G8Y)

(no "PROSITE Motif" information available for 2G8Y)

(no "Exon" information available for 2G8Y)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:359
 aligned with HCXB_ECOLI | P30178 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:359
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352         
           HCXB_ECOLI     3 SGHRFDAQTLHSFIQAVFRQMGSEEQEAKLVADHLIAANLAGHDSHGIGMIPSYVRSWSQGHLQINHHAKTVKEAGAAVTLDGDRAFGQVAAHEAMALGIEKAHQHGIAAVALHNSHHIGRIGYWAEQCAAAGFVSIHFVSVVGIPMVAPFHGRDSRFGTNPFCVVFPRKDNFPLLLDYATSAIAFGKTRVAWHKGVPVPPGCLIDVNGVPTTNPAVMQESPLGSLLTFAEHKGYALAAMCEILGGALSGGKTTHQETLQTSPDAILNCMTTIIINPELFGAPDCNAQTEAFAEWVKASPHDDDKPILLPGEWEVNTRRERQKQGIPLDAGSWQAICDAARQIGMPEETLQAFCQQLAS 361
               SCOP domains d2g8ya_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2g8yA01 A:3-63,A:310-361                                     2g8yA02 A:64-281 Hypothetical oxidoreductase yiak; domain 2                                                                                                                                                               2g8yA03 A:282-309           2g8yA01 A:3-63,A:310-361                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee...hhhhhhhhhhhh..eeeeeeee....................eeeeeee..eeeeeeee.....hhhhhhhhhhhh.......ee.....ee.hhhhhh.....ee....hhhhhhhhhhhhhhh.........hhhhh.......eeeeeeeee.hhhh...hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhheeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g8y A   3 SGHRFDAQTLHSFIQAVFRQmGSEEQEAKLVADHLIAANLAGHDSHGIGmFPSYVRSWSQGHLQINHHAKTVKEAGAAVTLDGDRAFGQVAAHEAmALGIEKAHQHGIAAVALHNSHHIGRIGYWAEQCAAAGFVSIHFVSVVGIPmVAPFHGRDSRFGTNPFCVVFPRKDNFPLLLDYATSAIAFGKTRVAWHKGVPVPPGCLIDVNGVPTTNPAVmQESPLGSLLTFAEHKGYALAAmCEILGGALSGGKTTHQETLQTSPDAILNCmTTIIINPELFGAPDCNAQTEAFAEWVKASPHDDDKPILLPGEWEVNTRRERQKQGIPLDAGSWQAICDAARQIGmPEETLQAFCQQLAS 361
                                    12        22|       32        42        52        62        72        82        92     | 102       112       122       132       142      |152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342    |  352         
                                               23-MSE                       52-MSE                                        98-MSE                                            149-MSE                                                                220-MSE               242-MSE                       272-MSE                                                                    347-MSE

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with HCXB_ECOLI | P30178 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        
           HCXB_ECOLI     4 GHRFDAQTLHSFIQAVFRQMGSEEQEAKLVADHLIAANLAGHDSHGIGMIPSYVRSWSQGHLQINHHAKTVKEAGAAVTLDGDRAFGQVAAHEAMALGIEKAHQHGIAAVALHNSHHIGRIGYWAEQCAAAGFVSIHFVSVVGIPMVAPFHGRDSRFGTNPFCVVFPRKDNFPLLLDYATSAIAFGKTRVAWHKGVPVPPGCLIDVNGVPTTNPAVMQESPLGSLLTFAEHKGYALAAMCEILGGALSGGKTTHQETLQTSPDAILNCMTTIIINPELFGAPDCNAQTEAFAEWVKASPHDDDKPILLPGEWEVNTRRERQKQGIPLDAGSWQAICDAARQIGMPEETLQAFCQQLAS 361
               SCOP domains d2g8yb_ B: automated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2g8yB01 B:4-63,B:310-361                                    2g8yB02 B:64-281 Hypothetical oxidoreductase yiak; domain 2                                                                                                                                                               2g8yB03 B:282-309           2g8yB01 B:4-63,B:310-361                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee...hhhhhhhhhhhh..eeeeeeee....................eeeee.......eeeee.....hhhhhhhhhhh........ee.....ee..hhhhhh....ee....hhhhhhhhhhhhhhh.........hhhhh.......eeeeeeeee.hhhh...hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhheeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g8y B   4 GHRFDAQTLHSFIQAVFRQmGSEEQEAKLVADHLIAANLAGHDSHGIGmFPSYVRSWSQGHLQINHHAKTVKEAGAAVTLDGDRAFGQVAAHEAmALGIEKAHQHGIAAVALHNSHHIGRIGYWAEQCAAAGFVSIHFVSVVGIPmVAPFHGRDSRFGTNPFCVVFPRKDNFPLLLDYATSAIAFGKTRVAWHKGVPVPPGCLIDVNGVPTTNPAVmQESPLGSLLTFAEHKGYALAAmCEILGGALSGGKTTHQETLQTSPDAILNCmTTIIINPELFGAPDCNAQTEAFAEWVKASPHDDDKPILLPGEWEVNTRRERQKQGIPLDAGSWQAICDAARQIGmPEETLQAFCQQLAS 361
                                    13        23        33        43        53        63        73        83        93    |  103       113       123       133       143     | 153       163       173       183       193       203       213      |223       233       243       253       263       273       283       293       303       313       323       333       343   |   353        
                                              23-MSE                       52-MSE                                        98-MSE                                            149-MSE                                                                220-MSE               242-MSE                       272-MSE                                                                    347-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: L-sulfolactate dehydrogenase-like (12)

Superfamily: L-sulfolactate dehydrogenase-like (12)

Family: automated matches (5)

Protein domain: automated matches (5)

Escherichia coli K-12 [TaxId: 83333] (1)

1a	d2g8ya_	A:
1b	d2g8yb_	B:

(no "Pfam Domain" information available for 2G8Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HCXB_ECOLI | P30178)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:223 - Pro A:224	[ RasMol ]
		Ser B:223 - Pro B:224	[ RasMol ]

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	2g8y
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Description

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Ligands, Modified Residues, Ions (5, 37)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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